Searches the ENCODE genomics database, builds chromatin accessibility maps, runs batch analyses across many experiments, and helps with bioinformatics tool installation and ENCODE citations, all from natural language in Claude Code.
@ammawlaBuild comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE…
@ammawlaGuide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE…
@ammawlaInstall bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages…
@ammawlaGuide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need cell-type-specific…
@ammawlaGenerate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE data, create…
@ammawlaGuide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if variants in…
@ammawlaCompare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns.…
@ammawlaCross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl,…
@ammawlaTrack exact provenance for every operation on ENCODE data — tool versions, reference files, scripts, parameters, and timestamps —…
@ammawlaUse ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to…
@ammawlaDownload ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to download data…
@ammawlaQuery the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene…
@ammawlaExecute ENCODE ATAC-seq pipeline from FASTQ to accessibility peaks with Tn5 correction, Bowtie2, and MACS2
@ammawlaExecute ENCODE ChIP-seq pipeline from FASTQ to peaks and signal tracks using BWA-MEM, MACS2, and IDR
@ammawlaExecute CUT&RUN pipeline from FASTQ to peaks with Bowtie2, SEACR, and spike-in normalization
@ammawlaExecute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints using BWA, Hotspot2, and HINT (RGT)
@ammawlaExecute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls using BWA, pairtools, Juicer, and HiCCUPS
@ammawlaExecute ENCODE RNA-seq pipeline from FASTQ to gene quantification using STAR 2-pass alignment and RSEM/Kallisto
@ammawlaExecute ENCODE WGBS pipeline from FASTQ to methylation calls using Bismark and MethylDackel
@ammawlaList, search, and inspect ENCODE files by format, type, and assembly
@ammawlaGenerate ENCODE citations for publications, grants, and presentations
@ammawlaCheck if two ENCODE experiments are compatible for combined analysis
@ammawlaCross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
@ammawlaDownload ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
@ammawlaLog derived files and trace provenance back to ENCODE source data
@ammawlaStore, check, or clear ENCODE API credentials for restricted data
@ammawlaAssess ENCODE experiment quality using audit counts and replicate counts
@ammawlaSearch ENCODE experiments by assay, organ, biosample, or target
@ammawlaTrack ENCODE experiments locally with publications and provenance
@ammawlaShips with encode-toolkit: Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready…
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